Shared Resource 08: Genomics (GSR)

Ohio State University, Columbus OH

Investigators

Linked publications, trials & patents

Abstract

PROJECT SUMMARY – GENOMICS SHARED RESOURCE (GSR) The mission of the GSR is to support OSUCCC members and high-impact cancer research projects with genomics expertise, instrumentation and centralized resources to generate high-quality data. The GSR is a state- of-the-art genomics laboratory that has substantially increased capacity through expansion to shared resources at Nationwide Children’s Hospital. The GSR has the following Specific Aims: 1) sequence DNA and RNA templates using both next generation sequencing platforms (i.e. Ilumina HiSeq4000 and NovaSeq6000) and capillary Sanger sequencing and genotyping (via ABI 3730XL DNA Analyzers); 2) use sensitive molecular hybridization methods to detect and quantify RNA transcript expression levels and structures such as splicing and/or DNA copy numbers and variation, including digital (NanoString) and microarray (Affymetrix) platforms; and 3) perform polymerase chain reaction (PCR)-based amplification to detect, quantify and confirm copy number variants, single nucleotide variants, gene expression, and small insertion/deletion polymorphisms including quantitative PCR (QuantStudio 12K flex) and high-throughput digital and custom PCR assay (BiomarkHD and Juno) technologies. In 2018, the GSR partnered with the Institute for Genomic Medicine (IGM) at Nationwide Children’s Hospital (NCH) to expand our next-generation sequencing (NGS) technology services. The GSR co-Directors are Drs. Amanda Toland (MCC) and Richard Wilson (CB). The GSR provides essential genomics expertise and instrumentation to members of all five programs. During the current funding cycle, the GSR contributed to 338 publications (63 > 10 impact factor) and 94 grants from members of all five programs. We have been highly responsive to changing technology and user needs and, as a result, we now offer Sanger sample pick-up, cell line verification, and single-cell (sc) RNA sequencing. We also regularly host technology- based seminars or workshops to introduce new technology to OSUCCC members. With OSUCCC and institutional support, we have expanded our facilities to improve sequencing capabilities and to include nanofluidics liquid handlers and library preparation systems for sc-sequencing to provide state-of-the-art resolution in cancer biology and response to therapy. In the next funding cycle, the GSR will support the genomics needs of all OSU strategic priorities. Given the robust OSUCCC recruitment, demand for services and new technologies will increase. The GSR will expand its staff, instrumentation and services before capacity is reached. New services under development include isolation of circulating tumor cells for down-stream culturing and genomic profiling, purchasing an instrument and developing protocols for spatial transcriptomics, purchasing an instrument for sc-DNA sequencing, and optimizing protocols for other sc-genomics and low-input NanoString applications. The annual budget of the GSR is $2,634,443, yet the CCSG request is $231,495. As such, the GSR leverages extensive institutional support and seeks only 8.8% support from CCSG funds.